The Blue Samurai started slowly at Dushanbe Central Stadium, struggling to find their rhythm on a pitch which was almost bald.
And the AFC Asian Cup holders, who defeated Tajikistan 8-0 at home, faced a scare when midfielder Dilshod Vasiev hit the post with a sizzling shot in the 31st minute.
But Japan opened the scoring in the 36th minute when Kengo Nakamura's shot was saved by goalkeeper Alisher Tuychiev only for defender Yasuyuki Konno to pounce on the rebound for his first national team goal.
Second-half substitute Ryoichi Maeda added another in the 82nd minute after he received the ball at the edge of the area with four defenders in front of him, moved to the right and hit a shot into the net. Japan completed the victory in injury time with a fluid passing move finished off by Okazaki.
Japan's Italian coach Alberto Zaccheroni said: "For us, the result is the most important. Our team scores goals by creating many chances, not by creating only a few chances.
"The Middle Eastern and Central Asian teams are physically strong. On top of that, the pitch condition was very bad today. Personally, I feel that it is very difficult to play an away game in Asia, but we are the only team to score 12 goals against Tajikistan."
Japan will now be sure to qualify unless Korea DPR can maintain their faint hopes of reaching consecutive FIFA World Cups by claiming at least a point in Uzbekistan.